Authors	Article Title	Journal	Published Year	Status	DOI
Radomir M. Slominski, Chander Raman, Jake Y. Chen, and Andrzej T. Slominski	How cancer hijacks the body’s homeostasis through the neuroendocrine system and why		2022	in review
Andrzej T. Slominski, Radomir M. Slominski, Chander Raman, Jake Y. Chen, Mohammad Athar, Craig Elmets	Neuroendocrine signaling in the skin with a special focus on the epidermal neuropeptides	American Journal of Physiology-Cell Physiology	2022	in review
Min Gao, Shanrun Liu, Qi Wu, PingAr Yang, Alex Essman, Bao Luo, Oluwagbemiga A. Ojo, David Crossman, Michael R. Crowley, Ignacio Sanz, Jake Y. Chen, W. Winn Chatham, John D. Mountz*, and Hui-Chen Hsu*	High Dimensional Analysis Reveals IL-4R as a Protective Factor to Prevent DN2 B-cell Development in SLE	Immunology	2021	in review
Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, and Jake Y. Chen	Guest Editorial for Selected Papers from BIOKDD 2021	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2022	in press
Dongmei Sun, Thanh M. Nguyen, Robert J. Allaway, Jelai Wang, Verena Chung, Thomas V Yu, Michael Mason, Isaac Dimitrovsky, Lars Ericson, Hongyang Li, Yuanfang Guan, Ariel Israel, Alex Olar, Balint Armin Pataki, RA2 DREAM Challenge Community, Gustavo Stolovitzky, Justin Guinney, Percio S. Gulko, Mason B. Frazier, James C. Costello*, Jake Y. Chen*, and S. Louis Bridges, Jr.*	A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis	JAMA Network Open, 5(8):e2227423	2022	published	10.1001/jamanetworkopen.2022.27423
Christian T. Stackhouse, Joshua C. Anderson, Zongliang Yue, Thanh Nguyen, Nicholas J. Eustace, Lara Ianov, Catherine P. Langford, Jelai Wang, James R. Rowland III, Chuan Xing, Fady M. Mikhail, Eddy S. Yang, Anita B. Hjelmeland, C. Ryan Miller, Jake Y. Chen, G. Yancey Gillespie, Christopher D. Willey	A Novel in vivo Model of Glioblastoma Radiation Resistance Identifies Long Non-coding RNAs and Targetable Kinases,	JCI Insights, 7(16):e148717	2022	published	doi.org/10.1172/jci.insight.148717
Zhenyu Weng, Zongliang Yue, Yuesheng Zhu, and Jake Y. Chen*	DEMA: a Distance-bounded Energy-field Minimization Algorithm to Model and Layout Bio-molecular Networks with Quantitative Features.	Bioinformatics, Vol. 38, No. S1, ppi359–i368,	2022	published	doi.org/10.1093/bioinformatics/btac261
Jianyi Zhang*, Yuji Nakada, Yang Zhou, Wuming Gong, Eric Zhang, Erik Skie, Thanh Nguyen, Yuhua Wei, Meng Zhao, Wangping Chen, Jake Y. Chen, Gregory Walcott, Daniel Garry, Jiacheng Sun, and Syed Raza	Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time-window of Cardiomyocyte Proliferation and Myocardial Regeneration.	Circulation, No. 145, pp. 1744-1747	2022	published
Zongliang Yue, Radomir Slominski, Samuel Bharti, and Jake Y Chen*	PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool of High-throughput Functional Genomics Results.	Frontiers in Genetics, Vol. 13,	2022	published	doi.org/10.3389/fgene.2022.820361
Thanh Nguyen, Jacob Jeevan, Nuo Xu, and Jake Y. Chen*.	Polar Gini Curve: a Quantitative Technique to Discover Gene Expression Spatial Patterns from Single-cell Data.	Genomics, Proteomics, and Bioinformatics,	2022	published	doi.org/10.1016/j.gpb.2020.09.006
Carlene L. Zindl, Steven J. Witte, Vincent A. Laufer, Min Gao, Zongliang Yue, Karen M. Janowski, Baiyi Cai, Blake F. Frey, Daniel J. Silberger, Stacey N. Harbour, Duy Pham, Henrietta Turner, Fran E. Lund, Bruce A. Vallance, Alexander F. Rosenberg, Trenton R. Schoeb, Jake Y. Chen, Robin T. Hatton and Casey T. Weaver*	A Non-redundant Role for T cell-derived IL-22 in Antibacterial Defense of Colonic Crypts	Immunity. Vol. 55, No. 3, pp. 494-511.e11	2022	published
Thanh Minh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D Willey and Jake Y Chen*	Statistical Enrichment Analysis of Samples (SEAS): a General-purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.	Frontiers in Big Data, Vol. 4, No. 81	2021	published	doi.org/10.3389/fdata.2021.725276
D. Yan*, S. Thankachan and Jake Y. Chen*	Guest Editorial for Selected Papers From BIOKDD 2019.	IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 18, No. 3, pp. 809-810.	2021	published	doi.org/10.1109/TCBB.2021.3067071
Sweta B. Patel, Travis Nemkov, Davide Stefanoni, Gloria A. Benavides, Brittany L. Crown, Victoria R. Matkins, Virginia Camacho, Ashley T. Hoang, Danielle E. Tenen, Samuel L. Wolock, Jihye Park, Mahmoud A. Bassal, Li Ying, Zongliang Yue, Jake Y. Chen, Henry Yang, Daniel G. Tenen, Paul Brent Ferrell, Rui Lu, Victor Darley-Usmar, Angelo D’Alessandro, Ravi Bhatia, Robert S. Welner	Metabolic alterations mediated by STAT3 promotes drug persistence in CML.	Leukemia, Vol. 35, pp. 3371–3382.	2021	published
Andrzej T Slominski, Tae-Kang Kim, Shariq Qayyum, Yuwei Song, Zorica Janjetovic, Allen SW Oak, Radomir M Slominski, Chander Raman, Joanna Stefan, Carlos A Mier-Aguilar, Venkatram Atigadda, David K Crossman, Andriy Golub, Yaroslav Bilokin, Edith K Y Tang, Jake Y. Chen, Robert C Tuckey, Anton M Jetten, Yuhua Song	Vitamin D and Lumisterol Derivatives Can Act on Liver X Receptors (LXRs),	Scientific Reports, Vol. 11, No. 1:8002.	2021	published
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan*, and Jake Y. Chen*.	Linking Clinotypes to Phenotypes and Genotypes from Laboratory Test Results in Comprehensive Physical Exams.	BMC Medical Informatics and Decision Making, Vol. 21, Suppl 3: 51	2021	published	doi.org /10.1186/s12911-021-01387-z
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Dang, and Jake Y. Chen*	PAGER-CoV: A Comprehensive Collection of Pathways, Annotated-gene-lists, and Gene Signatures for Coronavirus Disease Studies.	Nucleic Acids Research, Vol. 49, No. D1	2021	published	doi.org/10.1093/nar/gkaa1094
Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, and Jake Y. Chen	Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System	ACM/IEEE Transactions on Computational Biology and Bioinformatics, Vol. 18, No. 2, pp. 731-744	2021	published	doi.org/10.1109/TCBB.2019.2920912
C.D. Willey, C.T. Stackhouse, J.R. Rowland, C.P. Langford, J.C. Anderson, L. Ianov, Z. Yue, T. Nguyen, A.B. Hjelmeland, Jake Y. Chen, G.Y. Gillespie	Multi-omic Exploration of Inherent and Acquired Radiation Resistance of Glioblastoma Patient-derived Xenografts	International Journal of Radiation Oncology Biology Physics, Vol. 108, No. 3, Suppl., pp. S40.	2020	published
Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, and Gregory P Walcott.	Identifying the Key Regulators that Promote Cell-cycle Activity in the Hearts of Early Neonatal Pigs after Myocardial Injury.	PLOS ONE	2020	published	doi.org/10.1371/journal.pone.0232963
Keshav K Singh, Gyneshwer Chaubey, Jake Y. Chen, and Prashanth Suravajhala.	Decoding SARS-CoV-2 Hijacking of Host Mitochondria in Pathogenesis of COVID-19	American Journal of Physiology-Cell Physiology	2020	published	doi.org/10.1152/ajpcell.00224.2020
Huixian Hong, Min Gao, Qi Wu, PingAr Yang, Shanrun Liu, Hao Li, Peter D. Burrows, Daniel Cua, Jake Y. Chen, Hui-Chen Hsu, and John D. Mountz.	IL-23 promotes a coordinated B-cell germinal center program for class-switch recombination to IgG2b in BXD2 mice	J. Immunology, Vol. 205(2), pp 346-358	2020	published
Da Yan, Xin Gao, Samah J. Fodeh, and Jake Y. Chen*	Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.	IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 17, No. 6, pp. 1832-1834.	2020	published
Syed A Muhammad, Hiba Ashfaq, Sidra Zafar, Fahad Munir, Muhammad B Jamshed, Jake Y. Chen, and Qiyu Zhang	Polyvalent Therapeutic Vaccine for Type 2 Diabetes Mellitus: Immunoinformatics Approach to Study Co-Stimulation of Cytokines and GLUT1 Receptors.	BMC Molecular and Cell Biology, Vol. 21(1):56	2020	published	doi.org/10.1186/s12860-020-00279-w
George Dobbins, Amit Patki, Dongquan Chen, Hemant K. Tiwari, Curtis Hendrickson, William J. Britt, Karen Fowler, Jake Y. Chen, Suresh B Boppana, and Shannon A Ross*.	Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.	BMC Infectious Disease, Vol. 19(1);1046	2019	published	doi.org/10.1186/s12879-019-4681-0
Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, and Jake Y. Chen*	Weighted in-Path Edge Ranking for Biomolecular Association Networks	Quantitative Biology, Vol. 7, pp 313-326.	2019	published
Zongliang Yue, Christopher D Willey, Anita B Hjelmeland, and Jake Y. Chen*	BEERE: a Web Server for Biomedical Entity Expansion, Ranking, and Explorations.	Nucleic Acids Research, gkz428	2019	published
Xiaowen Liu, Zongliang Yue, Yimou Cao, Lauren Taylor, Qing Zhang, Sung Wong Choi, Samir Hanash, Sawa Ito, Jake Y. Chen, Huanmei Wu, and Sophie Paczesny	A GVHD-free Antitumoral Signature Following Allogeneic Donor Lymphocyte Injection Identified by Proteomics and Systems Biology.	JCO Precision Oncology, Vol. 3, pp 1-11	2019	published
Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, and Nengjun Yi	Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.	BMC Bioinformatics, Vol. 20, p. 94.	2019	published	doi.org/10.1186/s12859-019-2656-1
Syed Aun Muhammad*, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, and Jake Y. Chen*	A Systematic Simulation-based Meta-analytical Framework for Prediction of Physiological Biomarkers in Alopecia.	Journal of Biological Research-Thessaloniki, Vol. 26, No. 2	2019	published	doi.org/10.1186/s40709-019-0094-x
Xin Gao, Jake Y. Chen, and Mohammed J. Zaki	Multiscale and Multimodal Analysis for Computational Biology.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2018	published
Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen*	“Super Gene Set” Causal Relationship Discovery from Functional Genomics Data.	ACM/IEEE Transactions on Computational Biology and Bioinformatics, Vol. 15, No. 6, pp. 1991-1998.	2018	published
Wuqiang Zhu, Eric Zhang, Meng Zhao, Zechen Chong, Chengming Fan, Yawen Tang, Jervaughn D. Hunter, Anton V. Borovjagin, Greggory P. Walcott, Jake Y. Chen, Gangjian Qin, Jianyi Zhang	Regenerative Potential of Neonatal Porcine Hearts.	Circulation, Vol. 138, No. 24, pp. 2809-2816. (IF = 18.88)	2018	published
Syed Aun Muhammad*, Jinlei Guo, Thanh Minh Nguyen, Xiaogang Wu, Baogang Bai, X Frank Yang, Jake Y. Chen*	Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins	Frontiers in Microbiology, Vol. 9, No. 380	2018	published	doi.org/10.3389/fmicb.2018.00380
Zongliang Yue, Qi Zheng, Micheal T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen*	PAGER 2.0: An Update to the Pathway, Annotated-list, and Gene-signature Electronic Repository for Network Biology	Nucleic Acids Research, Vol. 46, No. D1, pp. D668-D676	2018	published
Zongliang Yue, Itika Arora, Eric Zhang, Vincent Laufer, S. Louis Bridges, and Jake Y. Chen*	Repositioning Drugs by Targeting Network Modules: A Parkinson’s Disease Case Study	BMC Bioinformatics, Vol. 18, Suppl 14, 532.	2017	published
Baron Arnone, Jake Y. Chen, and Gangjian Qin	Characterization and Analysis of Long Non-Coding RNA (lncRNA) in in vitro- and ex vivo-derived Cardiac Progenitor Cells	PLOS ONE	2017	published
Vincent A. Laufer, Jake Y. Chen, S Louis Bridges Jr	Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.	Rheumatic Disease Clinics, Vol. 43, No. 3, pp. 449-466.	2017	published
Jake Y. Chen*, Ragini Pandey, and Thanh Nguyen	HAPPI-2: Constructing a Comprehensive Map of Human Annotated and Predicted Protein Interactions	BMC Genomics, Vol. 18, 182. (IF = 4.07)	2017	published
Syed Aun Muhammad*, Waseem Raza, Thanh Nguyen, Baogang Bai, Xiaogang Wu, and Jake Chen*	Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus.	Frontiers in Physiology, Vol. 8, No. 13,	2017	published	doi.org/10.3389/fphys.2017.00013
Fan Zhang and Jake Y. Chen*	A Method for Identifying Discriminative Isoform-Specific Peptides for Clinical Proteomics Application.	BMC Genomics, Vol. 17, Suppl. 7, 522.	2016	published
Xiaowen Liu, Zongliang Yue, Jeffrey Yu, Etienne Daguindau, KushiKushekhar, Qing Zhang, Yuko Ogata, Philip Gafken, Yoshihiro Inamota, Adam Gracon, David Wikes, John Hansen, Stephanie Lee, Jake Y. Chen, and Sophie Paczesny*	Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation	American Journal of Transplantation, Vol. 16, No. 8, pp. 2342-2351.	2016	published
Syed Aun Muhammad, Nighat Fatima, Nawazish-i-Husain Syed, XiaogangWu, X. Frank Yang, and Jake Y. Chen*	MicroRNA Expression Profiling of Human Respiratory Epithelium Affected by Invasive Candida infection	PLOS ONE, Vol. 10, No. 8, e0136454	2015	published
Zongliang Yue, Madhura Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael Neylon, Liugen Zhu, Timothy Ratliff, and Jake Y. Chen*	PAGER: Constructing PAGs and new PAG-PAG Relationships for Network Biology.	Bioinformatics, Vol. 31, No. 12, pp. i250-i257	2015	published
Hui Huang, Thanh Nguyen, Sara Ibrahim, and Jake Y. Chen*	DMAP: A next-generation connectivity map database towards drug repositioning applications. MCBIOS ’15 Special Issue	BMC Bioinformatics, Vol. 16, Suppl. 13, S4	2015	published
Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen*	A Method for Developing Regulatory Gene Set Networks to Characterize Complex Biological Systems.	BMC Genomics, Vol. 16, Suppl. 11, S4	2015	published
Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki	Knowledge Discovery Using Big Data in Biomedical Systems.	IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, No. 4, pp. 726-729.	2015	published
Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, and Jake Y. Chen*	SLDR: A Computational Technique to Identify Novel Genetic Regulatory Relationship.	BMC Bioinformatics, Vol. 15, Suppl. 11, S1	2014	published
Syed Aun Muhammad, Safia Ahmed, Amjad Ali, Hui Huang, Xiaogang Wu, X. Frank Yang, Anam Naz, Jake Y. Chen*	Prioritizing Drug Targets in Clostridium botulinum with a Computational Systems Biology Approach.	Genomics, Vol. 104, No. 1, pp. 24-35	2014	published
Xiaogang Wu, Mohammad Al Hasan, and Jake Y. Chen*	Pathway and Network Analysis in Proteomics	Journal of Theoretical Biology, Vol. 362, pp. 44-52	2014	published
Zongliang Yue, Zhan Xie, Ping Wan, and Jake Y. Chen	Computational Identification of De-centric Genetic Regulatory Relationships from Functional Genomic Data,	Lecture Notes in Bioinformatics, Vol. 8492, pp. 224-235.	2014	published
Tianxiao Huan, Xiaogang Wu, Zengliang Bai*, and Jake Y. Chen*	Seed-weighted Random Walk Ranking for Cancer Biomarker Prioritization: a Case Study in Leukemia.	International Journal of Data Mining and Bioinformatics, Vol. 9, No. 2, pp.135-148.	2014	published
Shubo Zhang, Jake Y. Chen, Jianan Rao, Shanghong Zhang, Daniel Wai Tin Chan, Guanghua Liu, Yang Xu, and Miao He	Genetic Variation Analysis of Hemagglutinin and Neuraminidase of Human Influenza A (H3N2) Virus in Hong Kong (1997-2006).	African Journal of Microbiology Research, Vol. 8, No. 18, pp. 1863-1898.	2014	published
Jake Y. Chen, Micheline Piquette-Miller, and BP Smith	Network Medicine: Finding the Links to Personalized Therapy	Clinical Pharmacology & Therapeutics, Vol. 94, No. 6, pp. 613-615.	2013	published
Fan Zhang, Jake Chen, Mu Wang, and Renee Drabier	A Neural Network Approach to Multi-biomarker Panel Discovery by High-throughput Plasma Proteomics Profiling of Breast Cancer.	BMC Proceedings, Vol. 7, Suppl. 7, S10	2013	published
Huajun Chen*, Tong Yu*, and Jake Y. Chen*	Semantic Web Meets Integrative Biology: A Survey.	Briefings in Bioinformatics, Vol. 14, No. 1, pp. 109-125.	2013	published
Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen*	Predicting Adverse Drug Reaction Profiles by Integrating Protein Interaction Networks with Drug Structures.	Proteomics, Vol. 13, No. 2, pp. 313-324	2013	published
Fan Zhang and Jake Y. Chen*	Breast Cancer Subtyping from Plasma Proteins.	BMC Medical Genomics, Vol 6, Suppl. 1, S6	2013	published
Hui Huang, Xiaogang Wu, Ragini Pandey, Jiao Li, Guoling Zhao, Sara Ibrahim, Jake Y. Chen*	C2Maps: A Network Pharmacology Database with Comprehensive Disease-Gene-Drug Connectivity Relationships.	BMC Genomics, Vol. 13, Suppl. 6, S17.	2012	published
Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan*, Jake Y. Chen*	PAGED: A Pathway and Gene-set Enrichment Database to Enable Molecular Phenotype Discoveries.	BMC Bioinformatics, Vol. 13, Suppl. 15, S2. (IF = 2.75)	2012	published
Paul Hale, Alfredo M. López-Yunez, Jake Y. Chen*	Genome-wide Meta-analysis of Genetic Susceptible Genes for Type-2 Diabetes	BMC Systems Biology, Vol. 6, Suppl. 3, S16	2012	published
Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li*, and Jake Y. Chen*	Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.	Journal of Integrative Bioinformatics, Vol. 9, No. 2, 213.	2012	published
John Springer, Fan Zhang, Peter Hussey, Charles Buck, Fred Regnier, and Jake Y. Chen*	Towards a Metadata Model for Mass-Spectrometry Based Clinical Proteomics.	Current Bioinformatics, Vol. 7, No. 3, pp. 246-254.	2012	published
Mohammad Al Hasan, Jun Huan, Jake Chen, and Mohammed J. Zaki	Biological Knowledge and Data Mining: An Editorial	Scientific Programming, Vol. 20, No. 1, pp. 1-2.	2012	published
Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen*	Predicting Adverse Side Effects of Drugs.	BMC Genomics, Vol. 12, Suppl. 5, S11.	2011	published
Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, and Jake Y. Chen*	Reordering Based Integrative Expression Profiling for Microarray Classification.	BMC Bioinformatics, Vol. 13, Suppl. 2, S1	2011	published
Jiliang Li, Fan Zhang, and Jake Y. Chen*	An Integrated Proteomics Analysis of Bone Tissues in Response to Mechanical Stimulation.	BMC Systems Biology, Vol. 5, Suppl. 3, S7.	2011	published
Fan Zhang and Jake Y. Chen*	HOMER: A Human Organ-specific Molecular Electronic Repository.	BMC Bioinformatics, Vol. 12, Suppl. 10, S4.	2011	published
Fengjun Li, Xukai Zou, Peng Liu, and Jake Y. Chen*	New Threats to Health Data Privacy.	BMC Bioinformatics, Vol. 12, Suppl. 12, S7	2011	published
Lijie Sun, Hong-Mei Li, Manfredo J. Seufferheld, Kent Walters, Venu Margam, Amber Jannasch, Naomi Diaz, Catherine P. Riley, Weilin Sun, Yueh-Feng Li, William M. Muir, Jun Xie, Jing Wu, Fan Zhang, Jake Y. Chen, Eric L. Barker, Jiri Adamec, & Barry R. Pittendrigh	Systems-scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine.	PLOS ONE, 6(4): e18215	2011	published
Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, and Jake Y. Chen*	Computational Analysis of Drought-stress Associated miRNAs and miRNA Co-regulation Network in Physcomitrella Patens	Bioinformatics, Genomics, and Proteomics, Vol. 9, No. 1-2, pp. 37-44.	2011	published
Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Sharon A. Meyer, Edward J. Perkins, and Jake Y. Chen*	A new Approach to Construct Pathway Connected Networks and Its Application in Dose Responsive Gene Expression Profiles of Rat Liver Regulated by 2,4DNT.	BMC Genomics, Vol. 11, Suppl. 3, S4.	2010	published
Fan Zhang and Jake Y. Chen*	Discovery of Pathway Biomarkers from Coupled Proteomics and Systems Biology Methods.	BMC Genomics, Vol. 11, Suppl. 2, S12	2010	published
Ao Zhou, Fan Zhang, and Jake Y. Chen*	PEPPI: A Peptidomic Database of Human Protein Isoforms for Proteomics Experiments.	BMC Bioinformatics, Vol. 11, Suppl. 6, S7	2010	published
Steve Naylor and Jake Y. Chen*	Unraveling Human Complexity and Disease with Systems Biology and Personalized Medicine.	Personalized Medicine, Vol. 7, No. 3, pp. 275-289.	2010	published
Tianxiao Huan, Xiaogang Wu, and Jake Y. Chen*	Systems Biology Visualization Tools for Drug Target Discovery.	Expert Opinion on Drug Discovery, Vol. 5, No. 5, pp. 425-439.	2010	published
Hong-Mei Li, Lijie Sun, Omprakash Mittapalli, William M. Muir, Jun Xie, Jing Wu, Brandon J. Schemerhorn, Amber Jannasch, Jake Y. Chen, Fan Zhang, Jiri Adamec, Larry L. Murdock, and Barry R. Pittendrigh	Bowman-Birk Inhibitor Affects Pathways Associated with Energy Metabolism in Drosophila melanogaster	Insect Molecular Biology, Vol. 19, No. 3, pp. 303-313.	2010	published
Stefano Lonardi and Jake Y. Chen*	Data Mining in Bioinformatics: Selected Papers from BIOKDD 2008	IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 2, pp. 195-196.	2010	published
Mingyi Wang and Jake Y. Chen*	A GMM-IG Framework for Selecting Genes as Expression Panel Biomarkers	Artificial Intelligence in Medicine, Vol. 48, No. 2-3, pp.75-82	2010	published
Jiao Li, Xiaoyan Zhu, and Jake Y. Chen*	Discovering Novel Breast Cancer Drug Candidates from Biomedical Literature.	International Journal of Data Mining and Bioinformatics. Vol. 4, No. 3, pp.241-255.	2010	published
Qian You, Shiaofen Fang, and Jake Y. Chen*	GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks.	Information Visualization, Vol. 9, No. 1, pp.1-12.	2010	published
Jiao Li, Xiaoyan Zhu, and Jake Y. Chen*	Building Disease-specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.	PLoS Computational Biology, Vol. 5, No. 7: e1000450.	2009	published
Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, and Jake Y. Chen*	HPD: An Online Integrated Human Pathway Database Enabling Systems Biology Studies.	BMC Bioinformatics, Vol. 10, Suppl. 11, S5	2009	published
Jake Y. Chen*, SudhaRani Mamidipalli, and Tianxiao Huan	HAPPI: an Online Database of Comprehensive Human Annotated and Predicted Protein Interactions.	BMC Genomics, Vol. 10, Suppl. 1, S16.	2009	published
Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshu Zhou, and Jake Y. Chen*	Finding Fractal Patterns in Molecular Interaction Networks: a Case Study in Alzheimer’s Disease.	International Journal of Computational Biology and Drug Design, Vol. 2, No. 4, pp. 340-352.	2009	published
Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, and Jake Y. Chen*	Semantic Graph Mining for Biomedical Network Analysis: an Overview.	Briefings in Bioinformatics, Vol. 10, No. 2, pp. 177-192.	2009	published
Huian Li and Jake Y. Chen*	Improved Biomedical Document Retrieval System with PubMed Term Statistics and Expansions.	International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, pp. 74-85.	2009	published
Sudipto Saha, Scott H. Harrison, and Jake Y. Chen*	Dissecting the Human Plasma Proteome and Inflammatory Response Biomarkers.	Proteomics, Vol. 9, No. 2, pp. 470-484.	2009	published
Jake Y. Chen, Mohammed Zaki, and Stefano Lonardi	BIOKDD 2008: A Workshop Report on Data Mining in Bioinformatics.	SIGKDD Explorations, Vol. 10, No. 2, pp. 51-53.	2008	published
Tianxiao Huan, Andrey Sivachenko, Scott H. Harrison, and Jake Y. Chen*	ProteoLens: a Visual Analytic Tool for Multi-scale Database-driven Biological Network Data Mining.	BMC Bioinformatics, Vol. 9, S5, pp. 1-13	2008	published
Sudipto Saha, Scott H. Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J. Arnold, Xiang Zhang, and Jake Y. Chen*	HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals.	BMC Medical Genomics, 2008, Vol. 1, 12. (IF = 2.66)	2008	published
Stefano Lonardi and Jake Y. Chen*	International Workshop on Data Mining in Bioinformatics (BIOKDD) 2007: Introduction.	Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6, pp. v-vi.	2008	published
Lee W. Ott, Katheryn A. Resing, Alecia W. Sizemore, Joshua W. Heyen, Ross R. Cocklin, Nathan M. Pedrick, H. Cary Woods, Jake Y. Chen, Mark G. Goebl, Frank A. Witzmann, and Maureen A. Harrington	Tumor Necrosis Factor-alpha and Interleukin-1 Induced Cellular Responses: Coupling Proteomic and Genomic Information.	Journal of Proteome Research, Vol. 6, Issue 6, pp. 2176-2185.	2007	published
Lavanya Dhanapalan and Jake Y. Chen*	A Case Study of Integrating Protein Interaction Data using Semantic Web Technology.	International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 286-302.	2007	published
Jake Y. Chen*, Zhong Yan, Changyu Shen, Dawn P. G. Brown, and Mu Wang	A Systems Biology Approach to The Study of Cisplatin Drug Resistance In Ovarian Cancers.	Journal of Bioinformatics and Computational Biology, Vol. 5, Issue 02A, pp. 383-405.	2007	published
Megan Sickmeier, Justin Hamilton, Tanguy LeGall, Vladimir Vacic, Marc Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir Uversky, Zoran Obradovic, A Keith Dunker	DisProt: The Database of Disordered Proteins	Nucleic Acids Research, Vol. 35 (Database issue): pp. 786-93.	2007	published
Tharam S. Dillon, Elizabeth Chang, Amandeep S. Sidhu, and Jake Y. Chen*	Ontologies for Bioinformatics I.	International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 261-267.	2007	published
Zsuzsanna Dosztányi, Jake Y. Chen, A. Keith Dunker, István Simon, and Peter Tompa	Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution,	Journal of Proteome Research, Vol. 5, Issue 11, pp. 2985-2995	2006	published
Changyu Shen, Lang Li, Jake Y. Chen*	A Statistical Framework to Discover True Associations from Multi-protein Complex Pull-down Proteomics Data Sets.	Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 2, pp. 436-43.	2006	published
Jake Y. Chen* and Andrey Y. Sivachenko	Data Mining in Protein Interactomics.	IEEE Magazine in Biology and Medicine, Vol. 24, No. 3, pp. 95-102.	2005	published
Susie Stephens, Jake Y. Chen, Marcel Davidson, Shiby Thomas, and Barry M. Trute	Oracle Database 10g: A Platform for BLAST Search and Regular Expression Pattern Matching in Life Sciences	Nucleic Acids Research, Vol. 33, Database Issue, pp. 675-679.	2005	published
Susie Stephens, Jake Y. Chen, and Shiby Thoma	ODM BLAST: Sequence Homology Search in the RDBMS.	IEEE Data Engineering Bulletin, Vol. 27, Issue 3, pp. 20-23	2004	published
Jake Y. Chen*	Book Review: Digital Code of Life—How Bioinformatics is Revolutionizing Science, Medicine, and Business.	Briefings in Bioinformatics, Vol. 5, Issue 3, pp. 305-307.	2004	published
Jake Y. Chen* and John Carlis	Genomic Data Modeling.	Information Systems, Vol. 28, Issue 4: (Special Issue on Data Management in Bioinformatics), pp. 287-310.	2003	published

Authors	Article Title	Conference or Workshop	Published Year	Status	DOI
Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, and Sidharth Kumar	GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web, Proceedings of Eurographics Symposium on Parallel Graphics and Visualization		2022	in press
James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John D. Osborne, Amy Y. Wang, S. Louis Bridges, Jr., Matt Wyatt, and Jake Y. Chen*	Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE)	Proceedings of the IEEE 21st International Conference on Information Reuse and Integration for Data Science (IRI), Las Vegas, NV, USA, 2020 pp. 194-200	2020	published	10.1109/IRI49571.2020.00035.
Jake Chen*, Michael Neylon, Zongliang Yue, Thanh Nguyen, Timothy Ratliff	Towards Constructing “Super Gene Sets” Regulatory Networks	Proceedings of the 2016 International Conference on Bioinformatics & Biomedicine, Shenzhen, China,	2016	published	10.1109/BIBM.2016.7822534
Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguen, and Jake Chen*	Predictive and Preventive Models for Diabetes Prevention using Clinical Information in Electronic Health Record	Proceedings of the 2015 International Conference on Bioinformatics & Biomedicine, Washington, DC, pp. 867-874.	2015	published
Thanh Nguyen, Junjie Chen, Dongxiang Ji, Xiaoru Sun, Chuandi Pan,* Chengshui Chen*, and Jake Y. Chen*	An Integrated Machine Learning and Network Analysis to Discover Marker Clinical Measurement in Lung Cancer	Proceedings of 2015 International Conference on Genome Medicine, eds. Le L & Pham S, Ho Chi Minh City, Viet Nam.	2015	published
Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen*	Constructing Regulatory Gene Set Network to Reveal Novel Insights into Biological Systems,	Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, Miami Beach, FL	2014	published	10.1109/ICCABS.2014.6863927
Xiaogang Wu and Jake Chen*	An Evaluation for Merging Signaling Pathways by Using Protein-Protein Interaction Data	Proceedings of IEEE International Workshop on Genomic Signal Processing and Statistics, Washington, DC	2012	published
David Johnson, Brandon Shafer, Jaehwan John Lee, and Jake Chen*	Multi-Biomarker Panel Selection on a GPU	Proceedings of IEEE International Conference on Electro/Information Technology, Indianapolis, IN.	2012	published
Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christopher Reinhard, Shuyu D. Li, Jake Y. Chen*	Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays	Proceedings of the Eighth Annual International Symposium on Integrative Bioinformatics, Hangfzhou, Zhejiang, China.	2012	published
Liang-Chin Huang and Jake Y. Chen*	A Network Biology Approach to Predicting Drug Cardiotoxicity	Proceedings of the International Conference on Bioinformatics & Biomedicine, Atlanta, GA, pp. 278-281.	2011	published
Jason McLaughlin, Qian You, Shiaofen Fang, and Jake Y. Chen*	TAO: Terrain Analytic Operators for Expert-Guided Data Mining Applications	Workshop on Visual Analytics in Healthcare, Providence, RI.	2011	published
Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne Mckenzie, Sunil Badve, and Jake Y. Chen*	Predicting Drug Efficacy Based on the Integrated Breast Cancer Pathway Model,	IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX.	2011	published
Xiaogang Wu and Jake Y. Chen*	Network Reordering Based Integrative Expression Profiling for Microarray Classification	2011 Great Lakes Bioinformatics Conference, Athens, OH.	2011	published
Xukai Zou*, Peng Liu*, and Jake Y. Chen*	Personal Genome Privacy Protection with Feature-based Hierarchical Dual-stage Encryptions,	2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX.	2011	published
Fan Zhang and Jake Y. Chen*	Novel Protein Isoform Biomarker Identifications from Proteomes	2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong.	2010	published
Hui Huang, Xiaogang Wu, Shuyu Li, Sara Ibrahim, Taiwo Ajumobi, and Jake Y. Chen*	Evaluate Drug Effects on Gene Expression Profiles with Connectivity Maps	2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong.	2010	published
Fan Zhang and Jake Y. Chen*	Proteome-scale Protein Isoform Characterization with High-Performance Computing	2010 Microsoft eScience Workshop Proceedings, Berkeley, CA.	2010	published
Fengjun Li, Jake Y. Chen, Xukai Zou, and Peng Liu	New Privacy Threats in Healthcare Informatics: When Medical Records Join the Web	Ninth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2010) at the International Conference on Knowledge Discovery and Data Mining, Washington, DC.	2010	published
Fan Zhang, Mu Wang, and Jake Y. Chen*	Breast Cancer Plasma Protein Biomarker Discovery by Coupling LC-MS/MS Proteomics and Systems Biology	Proceedings of the ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY.	2010	published
Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen*	Random Walk Ranking Guided by Disease Association Networks for Lung Cancer Biomarker Discovery,	Proceedings of the International Symposium on Biocomputing, Vol. 1, No. 33, pp. 1-8.	2010	published
Jieun Jeong and Jake Y. Chen	RIC: Ranking with Interaction Chains and its Applications in Computational Clinical Proteomics Studies	Proceedings of the International Conference on Bioinformatics & Biomedicine, pp. 216-221.	2009	published
Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen*	SWRWR: Seed-weighted Random Walks Ranking Method and Its Application to Leukemia Cancer Biomarker Prioritizations	IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 220-225.	2009	published
Fan Zhang and Jake Y. Chen*	A Neural Network Approach to Multi-biomarker Panel Development Based on LC/MS/MS Proteomics Profiles: A Case Study in Breast Cancer,	Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems, pp. 1-6	2009	published	10.1109/CBMS.2009.5255456.
Hui Huang, Jiao Li, and Jake Y. Chen*	Disease Gene-fishing in Molecular Interaction Networks: a Case Study in Colorectal Cancer	Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419.	2009	published
Xiaogang Wu, Ragini Pandey, and Jake Y. Chen*	Network Topological Reordering Revealing Systemic Patterns in Yeast Protein Interaction Networks	Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419.	2009	published
Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Vaka, and Jake Y. Chen*	Visualizing a Correlative Multi-level Graph of Biology Entity Interactions	Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp.304-309.	2009	published
John Springer and Jake Y. Chen*	Toward Ontology-Driven Omics Data Integration in Current Database Management Systems	Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp. 292-297.	2009	published
Jiao Li, Pamela Crowell, and Jake Y. Chen*	Construct Anticancer Drug-Drug Correlation Network	Proceedings of the 24th Annual ACM Symposium on Applied Computing, Vol. 2, pp. 771-775	2009	published
Mingyi Wang and Jake Y. Chen*	Gene Selection using the GMM-IG Framework based Integrative Analysis.	IEEE Proceedings of the International Conference on Biomedical Engineering and Informatics, Vol.1, pp. 292-296.	2008	published
Harini Kasamsetty, Xiaogang Wu, and Jake Y. Chen*	An Integrative Human Pathway Database for Systems Biology Applications.	Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1297-1301.	2008	published
Jiao Li, Xiaoyan Zhu, and Jake Y. Chen*	Mining Disease-Specific Molecular Association Profiles from Biomedical Literature: A Case Study.	Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1287-1291.	2008	published
Jake Y. Chen*, Changyu Shen, Zhong Yan, Dawn P. G. Brown, and Mu Wang	A Systems Biology Case Study of Ovarian Cancer Drug Resistance.	Computational Systems Bioinformatics: CSB2006 Conference Proceedings, edited by Peter Markstein and Ying Xu, Series on Advances in Bioinformatics and Computational Biology, Vol. 4, pp. 389-398.	2006	published
Jake Y. Chen*, Sarah L. Pinkerton, Changyu Shen, and Mu Wang	An Integrated Computational Proteomics Method to Extract Protein Targets for Fanconi Anemia Studies.	Proceedings of the 21st Annual ACM Symposium on Applied Computing, Dijon, France, Vol. I, pp. 173-179.	2006	published
Jake Y. Chen*, Changyu Shen, and Andrey Sivachenko	Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data	Pacific Symposium on Biocomputing, Vol. 11, pp. 367-378.	2006	published
Changyu Shen, Lang Li, Jake Y. Chen*	Discover True Association Rates in Multi-protein Complex Proteomics Data Sets.	Proceedings of the IEEE Computational Systems Biology Bioinformatics Conference, Stanford University, Stanford, CA, Vol. 1, pp. 167-174	2005	published
Jake Y. Chen*, John Carlis, and Ning Gao	A Method for Conquering Complex Biological Database Queries.	Proceedings of the 20th Annual ACM Symposium on Applied Computing, Santa Fe, NM, Vol. I, pp. 110-114	2005	published
Jake Y. Chen*	Experience with Processing and Exploration of High-throughput Protein Interaction Data, Session on Systems Biology and Bioinformatics.	Proceedings of the Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, Vol. VII, pp. 41-45.	2004	published
Jake Y. Chen*, Andrey Y. Sivachenko, and Lang Li	High-throughput Protein Interactome Data: Minable or Not?	High-throughput Protein Interactome Data: Minable or Not?	2004	published
Jake Y. Chen*, Andrey Y. Sivachenko, Russell Bell, Connie Kurschner, Irene Ota, and Sudhir Sahasrabudhe	Initial Large-scale Exploration of Protein-protein Interactions in the Human Brain.	Proceedings of the IEEE CSB Bioinformatics Conference, Stanford University, Stanford, CA, published by IEEE Computer Society Press, pp. 229-234	2003	published
Jake Y. Chen* and John Carlis	Similar_Join: Extending DBMS with a Bio-specific Operator	Proceedings of the 18th ACM Symposium on Applied Computing, Melbourne, Florida, pp. 109-114.	2003	published
Jake Y. Chen* and John Carlis	Managing Bioinformatics Challenges in Expression Microarray Sequence Selection Projects.	Proceedings of the Second Chinese Conference on Bioinformatics, Beijing, China.	2002	published
Jake Y. Chen* and John Carlis	A High-density Microarray Case Study of Query Modeling In Bioinformatics.	Proceedings of the International Conference on Bioinformatics 2002, Bangkok, Thailand.	2002	published
Yue Chen*, Libby Shoop, John Carlis, and John Riedl	A High-throughput System to Resolve Inconsistent Reading Frame Predictions for Expressed Sequence Tags.	Proceedings of Workshop on Inconsistency in Data and Knowledge at the International Joint Conference on Artificial Intelligence (IJCAI), Seattle, WA.	2001	published